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I´m creating a spatial map of trees based on x-y location using the spatstat package and the ppp function. I´ve been able to do this and the size of each point is based on tree diameter. What I haven´t been able to do, and I hope to find some help here, is to create a legend that allows me to show these different circles and also include the 6 tree species within the plot. Here is the code I´m using:

df <- subset(plots, plots$spp == "DF")  # Douglas-fir

dfx <- as.numeric(as.character(df$x))
dfy <- as.numeric(as.character(df$y))
dfd <- as.numeric(as.character(df$d))

dfp <- ppp(dfx, dfy, window = owin(c(0, 100), c(0, 100)),
                  unitname=c("metres","metres"), marks = dfd)
par(mar = c(2, 2, 2, 2))                                           
plot(dfp, main = "", cex = 0.8, markscale = 0.04, 
     bg = rgb(0.1,0.9,0.3,0.5), fg = "black")

I have a similar structure for every species in the plot (wh for Western Hemlock and the code is the same...)

Thanks!

markalex
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Emilio Vilanova
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  • Just to clarify: You want each species to be plotted with a different colour and then include a legend connecting species names with colours? – Ege Rubak Sep 22 '16 at 05:29

1 Answers1

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First collect all the data into a single ppp object using superimpose. For example if you have Douglas Fir dfp and Western Hemlock whp then

  X <- superimpose(DF=dfp, WH=whp)

creates a point pattern X in which each point has two mark values, the species and the diameter. For convenience, change the mark column names:

  colnames(marks(X)) <- c("diameter", "species")

Next determine the plot symbol map for the diameters (without plotting anything):

  dmap <- plot(subset(X, select=diameter), do.plot=FALSE)

Next pick a set of colours for the different species, e.g.

  spec <- levels(marks(X)$species)
  scol <- c("red", "blue")
  smap <- symbolmap(inputs=spec, col=scol)

Now plot the species in separate colours using the diameter scale map:

  plot(Window(X), main="The main title")
  for(i in seq_along(spec)) {
     sy <- update(dmap, col=scol[i])
     Xi <- subset(X, species==spec[i], select=diameter)
     plot(Xi, add=TRUE, symap=sy)
  }

Finally plot the two symbol maps dmap and smap in the places you want by using plot(dmap, add=TRUE, xlim=..., ylim=...) and so on.

In future this will be automated, but it hasn't been implemented yet.

Adrian Baddeley
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  • The [superimpose] worked perfect for creating one unique ppp object. Nevertheless, I've been getting error messages for the [ dmap <- plot(subset(X, select=diameter), do.plot=FALSE)]. The error is "Error in subset.default(X, select = diameter) : argument "subset" is missing, with no default". – Emilio Vilanova Sep 24 '16 at 22:19
  • [superimpose] worked perfect for creating one unique ppp object. Yet, I've been getting error messages for the [dmap <- plot(subset(X, select=diameter), do.plot=FALSE)]. The error is "Error in subset.default(X, select = diameter) : argument "subset" is missing, with no default". I tried using the spit function but didn't work either. The symbolmap function belongs to ggplot? I'm kinda new on all of this and getting confused with error of "unable to locate symbolmap". I also had error in sy: Error en update.default(dmap, col = scol[X1i]) : need an object with call component – Emilio Vilanova Sep 24 '16 at 22:28
  • The error messages indicate either that spatstat was not loaded, or that X was not a ppp object. You need to type library(spatstat) before executing this code. Also ensure that the correct object X, as created in the first line of code, is being used in the third line of code. If it still doesn't work, please post a minimal example. – Adrian Baddeley Oct 25 '16 at 04:36